A low grade misfire will not trip a CEL. I would change the plugs and boots to start with, at 91k and 13+ years they are due. However, if the tranny fluid is dark it may be on its way out. When the fluid was changed, was a complete exchange done or was it just a pan drop?

Like GLC said, Plugs and boots for sure. It very well might save you the cost of a transmission. I have read many posts over the years where people are convinced its the torque converter or transmission and everything clears up with the ignition system tune up.

Fluid Change
 

@GLC - Pan drop and filter. Will do plugs and boots to start with. I've ready many different posts here about various boots, suppliers, etc...

Recommendations for the boots and plugs for the '02 4.6L?

Motorcraft plugs.

Absolutely Motorcraft plugs.

PM sent.

Let me know if I can help you with anything at all from advice to whatever.

Take care
D

A pan drop only got about 1/3 of the old fluid out, that's why it's dark again. Do a complete exchange with a machine. Should take about 14 quarts, pan only holds 5 quarts. Most of the rest of it is in the torque converter.

Motorcraft plugs, no antiseize, 28 ft/lb torque. Boot/spring kits are not brand-critical, just use a bit of dielectric grease in the boots, taking care not to get grease on the springs.